couple questions on my first box.

alright im making/mostly done with a box for 2 12 inch kicker l5's i made it out of mdf of course but i'm in autobody at hs and i need a project so i'm bondoing all of the corners and seams and screws and plan on leaving the open smooth areas just wood, but i also plan on painting it with car paint and i was told that the primer/paint will soak into the wood? anyone had any experience with this? also what do you guys think about using bondo on my wood box? its working well so far to smooth everything out. i'm just not sure how long it will stick/stay. what do you guys think?